Rendering two layers simultaneously glitch
You can simply use object index

This way, you can put all the objects on one layer, and still separate them for compositing.

It's easy


Switch your objects pass index.
Enable object index pass in the render passes
Use an ID mask node to create a mask of those objects.


Keep in mind

You can then try something like a mix node in the way shown to separate those objects on a black background. Keep in mind, that the output of the ID Mask node is like an alpha mask. Wherever that object is in the render, the output will be 1, wherever it is not, the output will be 0.

See the illustration below.



Here is an example of using this method to apply an effect. (the image shown under the composite nodes is the original.)